I see you have your ow opinion on this. Well tastes differ
Here's what I do. A foloder - is a project or depertment - whatever you like it to be. For me this is the beauty of it. I can create a tasks an put it into let's say "Mega Web-site design" folder. This is how I organize my tasks by projects. At the same time I put it into the "Marketing" folder. This is how I organize my tasks by department.

Flexibility rules!